update workflow

fgcz · Nov 14, 2024 · 769a90a · 769a90a
1 parent f2b6f10
commit 769a90a
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk b/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk
@@ -1,3 +1,6 @@
+# TODO some of these might be more relevant if only using `calibration.csv`, i.e. excluding standards
+
+
 rule qc_table_marker_surroundings_baseline:
     input:
         imzml=multiext("{sample}/processed", ".imzML", ".ibd"),

diff --git a/src/depiction_targeted_preproc/workflow/rules/rules_vis.smk b/src/depiction_targeted_preproc/workflow/rules/rules_vis.smk
@@ -2,7 +2,7 @@ rule vis_images:
     input:
         imzml=multiext("{sample}/calibrated", ".imzML", ".ibd"),
         config="{sample}/pipeline_params.yml",
-        mass_list="{sample}/panels/full.csv",
+        mass_list="{sample}/panels/full_visualize.csv",
     output:
         hdf5="{sample}/images_default.hdf5",
     # TODO how can i pass n-jobs nicely here